This is for study and training for class Bioinformatics in Action 2024, Tsinghua University

Getting started

4 steps of bioinformatics

Question

Top 5 questions in Science 2005

1. what is the universe made of ?
2. what is the biological basis of consciousness?
3. why do humans have so few genes?
4. to what extent are genetic variation and personal health linked?
5. can the laws of physics be unified?

Top 3 philosophy questions

• what is life
• what is mind
• how universe works

Information

Images

• Fluorescences
• Locations
• 3D structures
• docking

Sequence

• DNA-seq

• RNA-seq

• Epigenetics

  • DNAase
  • Methylation
  • Histone modifications: ChIP-seq

• Interaction

  • Protein-DNA: ChIP-seq
  • Protein-RNA: CLIP-seq
  • DNA-RNA: Grid-seq

Analysis

two keys: Data Clean & Feature Extraction

Modeling

Types

• Math
  • Eg: $y=w_0+\sum_{i=1}^{N}w_ix_i$
• physics
  • Eg: thermo dynamics
• …

Model VS Algorithm

	purpose	Method
Model	transform real problem into math	Math and physics
Algorithm	translate math into computer logic elegantly	Logic

The Fourth Paradigm

Study Schedule

Date	Class	My Own
week 1-4	Basic Linux, Blast	Get familiar with docker, linux and R
week 5-9	NGS Data analysis	Strictly following the class
week 10	Machine Learning & AI	review python and strictly following the class
week 11-16	SCS analysis	follow the class while fulfilling the extra tasks

Lecture 1

From Central dogma to bioinformatics

1D Study of DNA: How to Predict Genes from Raw Sequence?

A simple model

• given a stretch of genomic sequence
• preditc exons and introns

HMM(hidden Markov Model): Voice Recognition–>DNA Gene Finder: Grammars

2D study of RNA: Prediction of RNA Second Structure

language of RNA: base pair

• Trans-pairs
  • Interaction of 2 RNAs
• Cis-pairs
  • Folding of 1 RNA

SCFG(stochastic context-free grammar): RNA 2^nd^ structure prediction

• intron 被splicesome剪成lariat(套索)

3D study of protein: Preditcion 3D structure of Protein from sequence

Transformer(Large language model): Chat-GPT–>protein 3D structure

4D study of Precision Medicine: Early Cancer Screening

• 多组学多模态数据整合